Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012966.1 Corchorus olitorius cultivar O-4 contig12999, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12325
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:416 original size:127 final size:124
Alignment explanation
Indices: 203--442 Score: 317
Period size: 126 Copynumber: 1.9 Consensus size: 124
193 ATTCCCTAAA
* * *
203 AAAATGGTAAAGATAAAATAGTTGTAAAAATATTGAATTTAATTGAATAAAAATAGAAGTTTTGG
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAAGTTTT-G
*
268 TAAAATAAAACTGTAAAAGTTTAAATAAT-GTCATTTAAGAAATATATTTAATTAAAATAGT
65 TAAAATAAAACTGTAAAAGTTTAAA-AATGGT-ATTTAAAAAATATATTTAATTAAAATAGT
*
329 AAAATGGTAAAAATAAAATAGTTATAAAATATATT-AGATTTGATTAAATAAAAATAG-AGTTTT
1 AAAATGGTAAAAATAAAATAGTTATAAAA-ATATTGA-ATTTAATTAAATAAAAATAGAAGTTTT
* *
392 -TAATTGAGTAAAATTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTT
64 GTAA---AATAAAACTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTT
443 GAAAAATAAG
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
124 3 0.03
126 53 0.52
127 45 0.45
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (124 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAAGTTTTGT
AAAATAAAACTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTTAATTAAAATAGT
Found at i:1088 original size:31 final size:30
Alignment explanation
Indices: 1053--1148 Score: 138
Period size: 31 Copynumber: 3.1 Consensus size: 30
1043 ACTAAATACT
* *
1053 AAAAAATTCTCTTATATTTTTCTTTTGGGAC
1 AAAAAA-TCCCTTATGTTTTTCTTTTGGGAC
*
1084 AAAAAAATCCCTTATGTTTTTCTTTTGAGAC
1 -AAAAAATCCCTTATGTTTTTCTTTTGGGAC
1115 AAAAACATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAA-ATCCCTTATGTTTTTCTTTTGGGAC
1146 AAA
1 AAA
1149 TCAGTACCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
30 5 0.08
31 48 0.81
32 6 0.10
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (30 bp):
AAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:1314 original size:29 final size:30
Alignment explanation
Indices: 1272--1345 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
1262 CTCATTTTTG
* * *
1272 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTATCCCAAAACA
*
1301 AAACATAAGGGATTATTTTATCCCAAAAGCA
1 AAACATAAGGGATTAATTTATCCCAAAA-CA
1332 AAACATAAGGGATT
1 AAACATAAGGGATT
1346 TTTTTGAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTATCCCAAAACA
Found at i:3035 original size:11 final size:12
Alignment explanation
Indices: 3001--3041 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
2991 AAGCTGCAAA
*
3001 AACAAT-CAACA
1 AACAATACAACC
3012 ATACAATACAACC
1 A-ACAATACAACC
3025 AACAA-ACAACC
1 AACAATACAACC
3036 AACAAT
1 AACAAT
3042 TAAAGAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 12 0.46
12 9 0.35
13 5 0.19
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.10
Consensus pattern (12 bp):
AACAATACAACC
Found at i:3763 original size:20 final size:21
Alignment explanation
Indices: 3738--3782 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
3728 TACACTGCAC
3738 AACCAAAAACAAACAAA-CCA
1 AACCAAAAACAAACAAAGCCA
**
3758 AACCAAATTCAAACAAAGCCA
1 AACCAAAAACAAACAAAGCCA
3779 AACC
1 AACC
3783 GCGTCTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.62, C:0.31, G:0.02, T:0.04
Consensus pattern (21 bp):
AACCAAAAACAAACAAAGCCA
Found at i:4830 original size:45 final size:45
Alignment explanation
Indices: 4779--4867 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
4769 CTTGGTTGAT
*
4779 GGCGGAATTTCAAAGCAACAAGGTGAAGTCTTCATCTGGGTCGAC
1 GGCGGAATTGCAAAGCAACAAGGTGAAGTCTTCATCTGGGTCGAC
4824 GGCGGAATTGCAAAGCAACAAGGTGAAGTCTTCATCTGGGTCGA
1 GGCGGAATTGCAAAGCAACAAGGTGAAGTCTTCATCTGGGTCGA
4868 ATTCGATGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.21
Consensus pattern (45 bp):
GGCGGAATTGCAAAGCAACAAGGTGAAGTCTTCATCTGGGTCGAC
Found at i:6258 original size:195 final size:195
Alignment explanation
Indices: 5914--6279 Score: 567
Period size: 195 Copynumber: 1.9 Consensus size: 195
5904 GTGTTTATCA
* * *
5914 TAATGTAATGTACTTGCATATATTGCTAATTACAGATTGTAATGAGAATAGACTATTTATGCTTT
1 TAATGTAATGTACTTGCA-ATATTGCAAATTACAGATTGTAATGAGAATAAACTATTTATGCTTA
*
5979 ACCTCTGTTCTTGAGTCTACTTTGAAATCAAAGAAATTTCAATGCATATATACCAGAATTTTCAG
65 ACCTCTGTTCTTGACTCTACTTTGAAATCAAAGAAATTTCAATGCATATATACCAGAATTTTCAG
*
6044 TCTTTCATATGGCACCAAGACTTTGGGTATGATTCTGGTTTTTTGTGATCACTTATTTCTCCTAT
130 TCTTTCATATGGAACCAAGACTTTGGGTATGATTCTGGTTTTTTGTGATCACTTATTTCTCCTAT
6109 T
195 T
6110 TAATGTAATGTGA-TTGC-ATATTG-AAATTACAGATTGTAATGAGAATAAACTATTTATGCTTA
1 TAATGTAATGT-ACTTGCAATATTGCAAATTACAGATTGTAATGAGAATAAACTATTTATGCTTA
* * * * *
6172 ACCCCTCTGTTCTTGACTCTACTTTGAAATTAAAGGAATTTCAGTGCATGTATACCTGAATTTTC
65 A--CCTCTGTTCTTGACTCTACTTTGAAATCAAAGAAATTTCAATGCATATATACCAGAATTTTC
* *
6237 ATTCTTTGATATGGAACCAAGACTTTGGGTATGATTCTGGTTT
128 AGTCTTTCATATGGAACCAAGACTTTGGGTATGATTCTGGTTT
6280 CTTTTTCTTT
Statistics
Matches: 155, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
193 37 0.24
194 6 0.04
195 96 0.62
196 15 0.10
197 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (195 bp):
TAATGTAATGTACTTGCAATATTGCAAATTACAGATTGTAATGAGAATAAACTATTTATGCTTAA
CCTCTGTTCTTGACTCTACTTTGAAATCAAAGAAATTTCAATGCATATATACCAGAATTTTCAGT
CTTTCATATGGAACCAAGACTTTGGGTATGATTCTGGTTTTTTGTGATCACTTATTTCTCCTATT
Found at i:8979 original size:15 final size:15
Alignment explanation
Indices: 8959--8988 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8949 CCTGTCTTTG
8959 ATTGTTCTTGCTGCT
1 ATTGTTCTTGCTGCT
*
8974 ATTGTTGTTGCTGCT
1 ATTGTTCTTGCTGCT
8989 GTGTTTGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.23, T:0.53
Consensus pattern (15 bp):
ATTGTTCTTGCTGCT
Found at i:10017 original size:32 final size:30
Alignment explanation
Indices: 9966--10062 Score: 81
Period size: 32 Copynumber: 3.1 Consensus size: 30
9956 TTTTTCCTCA
* *
9966 CTGAACTT-CAAATCAGGACATTTTGCCCC
1 CTGAACTTCCAAATCAGGACATTCTACCCC
*
9995 TCTGAACTTCCAAAATCGGGACATTCTACCCC
1 -CTGAACTTCC-AAATCAGGACATTCTACCCC
* * *
10027 CTGAATTTCCCAATGTCAAGACA-TCTTACCCC
1 CTGAACTT-CCAA-ATCAGGACATTC-TACCCC
10059 CTGA
1 CTGA
10063 TGGAGGGGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
30 8 0.15
31 12 0.22
32 35 0.64
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.27
Consensus pattern (30 bp):
CTGAACTTCCAAATCAGGACATTCTACCCC
Done.